The gut microbiome consists of trillions of beneficial microbes that play a crucial role in digestion, nutrient absorption, immune function, and even mood regulation.
While a diverse gut microbiota supports overall health and well-being, microbial imbalances can contribute to chronic inflammation, poor gut health, mood disorders, and metabolic dysfunction.
Learn how your diet and lifestyle habits can impact gut microbe diversity and discover the best foods to help beneficial bacteria thrive.
What is the gut microbiome?
The gut microbiome refers to a vast community of microorganisms consisting primarily of bacteria, but also viruses, fungi, and yeasts, that reside within the human digestive tract.
These beneficial microbes colonize the gut at birth, and their composition and diversity are shaped by environmental factors, diet, and lifestyle habits throughout the lifespan.
The microbiome populates the entire digestive tract, from the mouth to the rectum. However, the most concentrated and diverse microbial populations are located in the large intestine, which offers an ideal environment for anaerobic bacteria to thrive.
The human gut microbiome is composed of trillions of organisms representing hundreds of species, and each person’s microbial makeup is unique.
Research published in Gastroenterology & Hepatology highlights, “The number of bacteria within the gut is approximately 10 times that of all of the cells in the human body, and the collective bacterial genome is vastly greater than the human genome.”1
Gut microbes form complex networks that not only interact with each other but also with the human host, influencing a wide range of bodily functions and organ systems.
Watch the video below to learn how to promote gut health by supporting microbial diversity.
How does the microbiome affect your overall health?
The gut microbiome plays a central role in maintaining overall health by influencing and regulating a wide range of bodily functions.
Certain beneficial microbes produce short-chain fatty acids (SCFAs), including acetate, propionate, and butyrate. These SCFAs serve as fuel for the cells lining the colon and help regulate inflammation, support gut barrier integrity, and influence metabolic pathways.
The microbiome also has a profound impact on the immune system. A large proportion of the body’s immune cells are located in the gut, where they constantly interact with the microbiome.
Gut microbes help train the immune system to distinguish between harmful invaders and beneficial microbes, reducing the risk of intestinal infections and autoimmune diseases.
Furthermore, the gut microbiome interacts with the central nervous system via a complex communication network known as the gut-brain axis, which can influence brain function and mood regulation.
Gut microbes also help regulate the production of key neurotransmitters such as dopamine and serotonin, which play essential roles in the body’s stress response and emotional regulation.
This explains why maintaining a diverse gut microbiome is not only important for physical health but also supports mental wellness, cognitive function, and emotional well-being.
Other important functions of the microbiome include:
- Recycling bile acids
- Synthesizing vitamin K
- Breakdown of dietary fibers
- Detoxification support
- Gut motility regulation
- Enhancing nutrient absorption
- Appetite and hunger control
- Modulating metabolic pathways
- Influencing weight and body composition
A study published in Microorganisms highlights that dysbiosis can impair key physiological functions, contributing to chronic inflammation, metabolic disorders, weakened immunity, digestive issues, and neurological conditions.2
Signs of an unhealthy gut microbiome
Even subtle imbalances in the gut microbiota can disrupt vital functions and contribute to long-term health issues.
Because gut microbes interact with almost every system in the body, signs of an unhealthy microbiome can vary widely, making it challenging to identify the root cause of symptoms.
These imbalances often manifest in seemingly unrelated ways, such as the skin, moods, metabolic dysfunctions, or poor immune defenses.
Common signs that may indicate an unhealthy gut microbiome include:
- Gas and bloating
- Irregular bowel movements
- Sugar cravings
- Unexplained weight changes
- Mood disorders
- Brain fog
- Fatique
- Food intolerances
- Frequent infections
- Skin rashes
Dysbiosis can also increase the risk of serious health issues, including inflammatory bowel diseases, insulin resistance, and diabetes, and it’s vital to consult a healthcare provider should you experience symptoms of imbalanced gut microbes.
Causes of an unhealthy gut microbiome
Many factors can disrupt the delicate balance of gut microbes by creating an environment that suppresses the growth of beneficial microbes while encouraging the overgrowth of harmful species.
Here are six common causes of an unhealthy gut microbiome.
1. Antibiotic use
Frequent or prolonged antibiotic use increases the risk of dysbiosis as these drugs don’t discriminate between harmful and beneficial bacteria, therefore disrupting microbial balance.
2. Poor dietary habits
Your dietary choices play a vital role in shaping the composition and diversity of your gut microbiome.
Alcohol, ultra-processed foods, added sugars, refined carbohydrates, and artificial sweeteners can promote the growth of potentially harmful bacterial strains while depriving beneficial microbes of the nutrients they need to thrive.
3. Chronic stress
Evidence published in Biofilms and Microbiomes found that physical and emotional stress can trigger changes in gut microbiome diversity.3
It’s believed that stress alters the communication between gut microbes and the central nervous system and disrupts digestive functions, creating an environment that favors the growth and proliferation of harmful bacteria.
4. Exposure to environmental toxins
Exposure to agricultural pesticides, herbicides, industrial chemicals, artificial preservatives, and heavy metals can trigger intestinal inflammation and immune responses, which can negatively impact the microbiome.
5. Sedentary lifestyle
Physical activity promotes digestive health, reduces inflammation, and supports the growth of beneficial gut microbes, and a lack of movement can lead to decreased microbial diversity and a less resilient gut environment.
6. Lack of sleep
Lack of sleep can disrupt the body’s sleep-wake cycle and circadian rhythm, which regulates various aspects of gut function and microbial activity.
This has been supported by research published in Sleep Medicine, highlighting that individuals with persistent sleep problems are more likely to develop microbial imbalances and associated health issues.4
How to promote a healthy microbiome
A healthy gut microbiome profoundly benefits overall health and well-being, supports optimal digestive functions, and reduces the risk of various chronic health issues.
Here are five ways to promote a diverse microbiota.
1. Prioritize pre- and probiotic foods
Incorporating both pre- and probiotic foods is one of the most effective strategies for supporting a balanced and diverse gut microbiome.
Fermented foods, such as sauerkraut, kimchi, kefir, Lactobacillus reuteri yogurt, and miso, are excellent sources of beneficial microbes that help populate the gut with probiotics.
Prebiotic foods provide dietary fibers that nourish gut bacteria by serving as a fuel source, helping them grow and thrive.
Some of the best prebiotic foods include:
- Garlic
- Leeks
- Onions
- Jerusalem artichokes
- Asparagus
- Dandelion greens
- Flaxseeds
2. Follow a nutritious low-carb diet
Opportunistic and potentially harmful bacteria thrive on sugars and refined carbohydrates, and following a low-carb diet can be a highly effective approach to rebalance the gut microbiome.
Healthy Keto® is a low-carb diet that focuses on nutritious whole foods, including fermented foods, nourishing fats, prebiotic-rich vegetables, and high-quality proteins, making it an ideal meal plan for supporting a balanced microbiome.
In addition, Healthy Keto avoids processed foods and artificial sweeteners, which have been linked to a greater risk of dysbiosis.
3. Practice intermittent fasting
Intermittent fasting, which involves alternating between periods of caloric restriction and time-restricted eating windows, offers a range of health benefits, including significant support for gut health.
A study published in Frontiers in Microbiology found that intermittent fasting was associated with beneficial changes in the gut microbiota, including enhanced diversity and gut microbe density.5
4. Support a healthy gut environment
A healthy gut microbiome relies on an internal environment that promotes microbial balance.
This includes maintaining optimal stomach acid levels, essential for preventing harmful bacteria from entering the gut. Bile flow is equally important, as it helps regulate the growth of microbes in the small intestine.
Low stomach acid or bile deficiency can disrupt microbial balance. Taking diluted apple cider vinegar or lemon water with a meal may help boost stomach acidity, and bitter foods such as arugula, dandelion greens, and radicchio can promote bile flow and gallbladder health.
Supporting overall gut functions and staying well-hydrated can help create the ideal conditions for a thriving and balanced gut ecosystem.
5. Get adequate sleep
Sleep is essential for gut health as it allows the repair of the intestinal lining, supports detoxification processes, and promotes microbial balance and diversity.
Create a calming bedtime routine, minimize screen exposure in the evening, and aim for seven to nine hours of uninterrupted sleep each night to give your gut and microbiome time to restore balance and function optimally.
Key takeaways
The gut microbiome houses trillions of beneficial microbes that play a vital role in digestion, nutrient absorption, immune function, and mental well-being.
Prioritizing probiotic and prebiotic foods, following a nutritious low-carb diet, and practicing intermittent fasting helps promote microbiota diversity and supports a healthy gut.
In addition, it’s vital to get adequate sleep, stay physically active, and support optimal digestion to create a gut environment that helps beneficial bacteria thrive.
FAQ
What is the gut microbiome?
The gut microbiome is a vast community of bacteria, fungi, and yeasts that reside primarily in the large intestine. These beneficial microbes play essential roles in digestive functions, immune system defense, nutrient production, and mood regulation.
What are the signs of an unhealthy gut microbiome?
Common signs of imbalanced gut microbes, also known as dysbiosis, include digestive issues such as gas and bloating, acid reflux, abdominal pain, and irregular bowel movements.
In addition, dysbiosis can manifest as fatigue, weight changes, low moods, skin problems, frequent infections, sleep disturbances, sugar cravings, and hormonal imbalances.
What causes an unhealthy gut microbiome?
Dietary factors such as alcohol, processed foods, artificial sweeteners, refined carbohydrates, and sugars can feed harmful bacteria while starving beneficial microbes of nutrients.
In addition, antibiotic use, lack of sleep, a sedentary lifestyle, and exposure to heavy metals and agricultural herbicides can negatively impact microbial populations and contribute to dysbiosis.
How do I repair my gut microbiome?
Consuming plenty of fermented foods rich in probiotics, such as sauerkraut, kimchi, miso, and kefir, helps populate the gut with beneficial microbes.
It’s equally important to eat plenty of fiber-rich vegetables to nourish gut microbes, follow a nutritious low-carb diet, and support healthy digestion by promoting optimal stomach acid levels and bile flow.
How long does it take to improve your gut microbiome?
How long it takes to improve the gut microbiome depends on the severity of microbial imbalance, dietary habits, and health status.
However, many people begin noticing improvements in gut health within a couple of weeks of making beneficial dietary and lifestyle changes.
Sources
- https://pmc.ncbi.nlm.nih.gov/articles/PMC3983973/ ?
- https://pmc.ncbi.nlm.nih.gov/articles/PMC6351938/#sec2-microorganisms-07-00014 ?
- https://www.nature.com/articles/s41522-024-00571-z ?
- https://www.sciencedirect.com/science/article/pii/S1389945721004354#sec6 ?
- https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.922727/full#h5 ?
